An ultrametric coalescent tree over the 24 MAGs in gut_counts, scaled to unit depth. Use it for the phylogenetic-diversity paths.
Format
A phylo object (see the ape package) with 24 tips whose
labels match the rows of gut_counts.
Examples
hilldiv(gut_counts, q = c(0, 1), tree = gut_tree)
#> Computing "neutral" and "phylogenetic" Hill numbers of "q0" and "q1".
#> ℹ 24 taxa across 12 samples.
#> <hilldiv3 result: neutral, phylogenetic>
#> 48 rows x 4 cols
#>
#> q sample type value
#> 1 0 ctrl01 neutral 24.000000
#> 2 1 ctrl01 neutral 12.329592
#> 3 0 ctrl02 neutral 24.000000
#> 4 1 ctrl02 neutral 14.784342
#> 5 0 ctrl03 neutral 24.000000
#> 6 1 ctrl03 neutral 11.832847
#> 7 0 ctrl04 neutral 23.000000
#> 8 1 ctrl04 neutral 11.266414
#> 9 0 ctrl05 neutral 24.000000
#> 10 1 ctrl05 neutral 10.035886
#> 11 0 ctrl06 neutral 24.000000
#> 12 1 ctrl06 neutral 13.277945
#> 13 0 trt01 neutral 24.000000
#> 14 1 trt01 neutral 11.888942
#> 15 0 trt02 neutral 24.000000
#> 16 1 trt02 neutral 8.350790
#> 17 0 trt03 neutral 24.000000
#> 18 1 trt03 neutral 15.681517
#> 19 0 trt04 neutral 23.000000
#> 20 1 trt04 neutral 11.671685
#> 21 0 trt05 neutral 23.000000
#> 22 1 trt05 neutral 9.043005
#> 23 0 trt06 neutral 23.000000
#> 24 1 trt06 neutral 10.901319
#> 25 0 ctrl01 phylogenetic 3.757442
#> 26 1 ctrl01 phylogenetic 2.156361
#> 27 0 ctrl02 phylogenetic 3.757442
#> 28 1 ctrl02 phylogenetic 2.105705
#> 29 0 ctrl03 phylogenetic 3.757442
#> 30 1 ctrl03 phylogenetic 2.035022
#> 31 0 ctrl04 phylogenetic 3.750466
#> 32 1 ctrl04 phylogenetic 2.263603
#> 33 0 ctrl05 phylogenetic 3.757442
#> 34 1 ctrl05 phylogenetic 1.881365
#> 35 0 ctrl06 phylogenetic 3.757442
#> 36 1 ctrl06 phylogenetic 2.159882
#> 37 0 trt01 phylogenetic 3.757442
#> 38 1 trt01 phylogenetic 2.135261
#> 39 0 trt02 phylogenetic 3.757442
#> 40 1 trt02 phylogenetic 1.649469
#> 41 0 trt03 phylogenetic 3.757442
#> 42 1 trt03 phylogenetic 2.212881
#> 43 0 trt04 phylogenetic 3.742870
#> 44 1 trt04 phylogenetic 1.853561
#> 45 0 trt05 phylogenetic 3.750466
#> 46 1 trt05 phylogenetic 1.906460
#> 47 0 trt06 phylogenetic 3.754523
#> 48 1 trt06 phylogenetic 1.996142